User Tools

Site Tools


trimmomatic-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

trimmomatic-software [2015/09/25 11:22]
joguya created
trimmomatic-software [2018/06/02 02:03] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 0.33+  * Version: 0.38
   * Added: September, 2015   * Added: September, 2015
 +  * Updated: June, 2018
   * Link: http://​www.usadellab.org/​cms/?​page=trimmomatic   * Link: http://​www.usadellab.org/​cms/?​page=trimmomatic
  
Line 13: Line 14:
 <​code>​$ module avail trimmomatic</​code>​ <​code>​$ module avail trimmomatic</​code>​
  
-Load and run trimmomatic+Load one version into your environment ​and run it
-<​code>​$ module load trimmomatic/​0.33+<​code>​$ module load trimmomatic/​0.38
 $ trimmomatic</​code>​ $ trimmomatic</​code>​
  
Line 20: Line 21:
 Notes from the sysadmin during installation:​ Notes from the sysadmin during installation:​
  
-<​code>​$ cd /tmp/ +<​code>​$ cd /tmp 
-$ wget http://​www.usadellab.org/​cms/​uploads/​supplementary/​Trimmomatic/​Trimmomatic-0.33.zip +$ wget http://​www.usadellab.org/​cms/​uploads/​supplementary/​Trimmomatic/​Trimmomatic-0.38.zip 
-cd Trimmomatic-0.33 +unzip Trimmomatic-0.38.zip 
-$ sudo mkdir -p /​export/​apps/​trimmomatic/​0.33 +$ sudo mkdir -p /​export/​apps/​trimmomatic/​0.38 
-$ sudo cp -rv . /​export/​apps/​trimmomatic/​0.33/ +$ sudo cp -r Trimmomatic-0.38/* /​export/​apps/​trimmomatic/​0.38</​code>​
-</​code>​+
  
-I created a wrapper shell script named ''​trimmomatic''​ to run Trimmomatic,​ otherwise, you'll have to specify a path to trimmomatic-0.33.jar—''​java -jar <path to trimmomatic.jar>​ ...''​—which is unfriendly. ''/​export/​apps/​trimmomatic/​0.33/​trimmomatic'':<​code>​ +Trimmomatic is distributed as a jar file and is not easy for users to run. I created a wrapper shell script named ''​trimmomatic'':​ 
-#​!/​usr/​bin/​env bash+ 
 +<​code>#​!/​usr/​bin/​env bash
  
 readonly PREFIX=$(dirname $0) readonly PREFIX=$(dirname $0)
-java -jar $PREFIX/​trimmomatic-0.33.jar $* +java -jar $PREFIX/​trimmomatic-0.38.jar $*</​code>​
-</​code>​+
trimmomatic-software.txt · Last modified: 2018/06/02 02:03 by aorth